Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001295.1 Hibiscus syriacus cultivar Beakdansim tig00002534_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 65339
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:4468 original size:22 final size:23
Alignment explanation
Indices: 4438--4490 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
4428 TATTTATTTA
4438 TATTATTAC-TATTATTATTATTC
1 TATTATTACTTATTATTA-TATTC
*
4461 TATT-TTACTTATTTTTATATTC
1 TATTATTACTTATTATTATATTC
4483 TATCTATT
1 TAT-TATT
4491 TTTATATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 12 0.46
23 12 0.46
24 2 0.08
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.64
Consensus pattern (23 bp):
TATTATTACTTATTATTATATTC
Found at i:4484 original size:55 final size:56
Alignment explanation
Indices: 4359--4497 Score: 135
Period size: 55 Copynumber: 2.5 Consensus size: 56
4349 TTTATAACTA
* * * *
4359 TTATTTTTATTTTTTTTTATATATATATATATATATAATTATATTTCTTATTTTCC
1 TTATTTTTATTTCTATTTATTTATATATATATATATAATTATATTTCTTATTTTAC
* *
4415 TT-TTTTTGTTTTCTATTTATTTATAT-TAT-TACTATTATTAT-TATTC-TATTTTAC
1 TTATTTTT-ATTTCTATTTATTTATATATATATA-TATAATTATAT-TTCTTATTTTAC
* *
4469 TTATTTTTATATTCTATCTATTTTTATAT
1 TTATTTTTAT-TTCTATTTATTTATATAT
4498 TTTCTTTTTA
Statistics
Matches: 68, Mismatches: 9, Indels: 12
0.76 0.10 0.13
Matches are distributed among these distances:
54 13 0.19
55 38 0.56
56 17 0.25
ACGTcount: A:0.25, C:0.06, G:0.01, T:0.68
Consensus pattern (56 bp):
TTATTTTTATTTCTATTTATTTATATATATATATATAATTATATTTCTTATTTTAC
Found at i:4509 original size:19 final size:17
Alignment explanation
Indices: 4425--4513 Score: 61
Period size: 17 Copynumber: 4.9 Consensus size: 17
4415 TTTTTTTGTT
*
4425 TTCTATTTATTTATATTA
1 TTCTATTTATTTTTA-TA
* *
4443 TTACTATTATTATTATTCTA
1 TT-CTA-T-TTATTTTTATA
* *
4463 TTTTACTTATTTTTATA
1 TTCTATTTATTTTTATA
*
4480 TTCTATCTATTTTTATA
1 TTCTATTTATTTTTATA
*
4497 TTTTCTTTTTATTTTTA
1 --TTCTATTTATTTTTA
4514 ATCTTTTTTA
Statistics
Matches: 54, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
17 23 0.43
18 2 0.04
19 18 0.33
20 5 0.09
21 6 0.11
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.69
Consensus pattern (17 bp):
TTCTATTTATTTTTATA
Found at i:4752 original size:17 final size:17
Alignment explanation
Indices: 4719--4764 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
4709 TTTTCATCTT
* *
4719 TTTTATTT-TTTTTTTG
1 TTTTATTTCATTTGTTG
4735 TTTTATTTCATTTGTTG
1 TTTTATTTCATTTGTTG
4752 TTTTATTTCATTT
1 TTTTATTTCATTT
4765 TATTTATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 8 0.30
17 19 0.70
ACGTcount: A:0.11, C:0.04, G:0.07, T:0.78
Consensus pattern (17 bp):
TTTTATTTCATTTGTTG
Found at i:11902 original size:24 final size:25
Alignment explanation
Indices: 11870--11919 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
11860 CAAATCCAAT
11870 CCGATCCAAAAA-AATAACCGAAAA
1 CCGATCCAAAAACAATAACCGAAAA
*
11894 CCGATCCAAAAACCGATAACCGAAAA
1 CCGATCCAAAAA-CAATAACCGAAAA
11920 AATCGAAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.52
26 11 0.48
ACGTcount: A:0.54, C:0.28, G:0.10, T:0.08
Consensus pattern (25 bp):
CCGATCCAAAAACAATAACCGAAAA
Found at i:16378 original size:45 final size:44
Alignment explanation
Indices: 16310--16415 Score: 176
Period size: 45 Copynumber: 2.4 Consensus size: 44
16300 TCTAGAATGC
16310 TTTAAATTTGAACAATTGCACAACTTTTAGTAGTGTATTTAGGG
1 TTTAAATTTGAACAATTGCACAACTTTTAGTAGTGTATTTAGGG
* *
16354 TTTAGAATTTAAACAATTGCACAACTTTTAGTAGTGTATTTGGGG
1 TTTA-AATTTGAACAATTGCACAACTTTTAGTAGTGTATTTAGGG
16399 TTTAAAATTTGAACAAT
1 TTT-AAATTTGAACAAT
16416 GTGCTATTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
44 4 0.07
45 52 0.91
46 1 0.02
ACGTcount: A:0.34, C:0.08, G:0.17, T:0.41
Consensus pattern (44 bp):
TTTAAATTTGAACAATTGCACAACTTTTAGTAGTGTATTTAGGG
Found at i:17576 original size:45 final size:44
Alignment explanation
Indices: 17512--17617 Score: 176
Period size: 45 Copynumber: 2.4 Consensus size: 44
17502 CAAATAGCAC
17512 ATTGTTCAAATTTTAAACCCCAAATACACTACTAAAAGTTGTGCA
1 ATTGTTCAAA-TTTAAACCCCAAATACACTACTAAAAGTTGTGCA
* *
17557 ATTGTTTAAATTCTAAACCCTAAATACACTACTAAAAGTTGTGCA
1 ATTGTTCAAATT-TAAACCCCAAATACACTACTAAAAGTTGTGCA
17602 ATTGTTCAAATTTAAA
1 ATTGTTCAAATTTAAA
17618 GCATTCTAGA
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
44 6 0.11
45 51 0.89
ACGTcount: A:0.41, C:0.17, G:0.08, T:0.34
Consensus pattern (44 bp):
ATTGTTCAAATTTAAACCCCAAATACACTACTAAAAGTTGTGCA
Found at i:26453 original size:59 final size:56
Alignment explanation
Indices: 26319--26489 Score: 180
Period size: 59 Copynumber: 2.9 Consensus size: 56
26309 GTATATACAT
* * * ** *
26319 ATAGTTTAGGATGAAATTGGAATGTCCAAAAAGTTTGGGGACCAATTTAGAATGGTC
1 ATAGTTTAGGATGAAATTGAAATATTC-AAAAGTTTGAAGAACAATTTAGAATGGTC
* * *
26376 ATAGTTCGAGGATGAAATTGAAATATTCAAAAGTTTGAAGAATAATTTAGAATTATGTC
1 ATAGTT-TAGGATGAAATTGAAATATTCAAAAGTTTGAAGAACAATTTAGAA-T-GGTC
* * *
26435 ATAGTTTATGGATGAAATTGAAATATTCAAAGGTTTTAAGAACCAATTTAAAATG
1 ATAGTTTA-GGATGAAATTGAAATATTCAAAAGTTTGAAGAA-CAATTTAGAATG
26490 AGGATCATAC
Statistics
Matches: 94, Mismatches: 15, Indels: 9
0.80 0.13 0.08
Matches are distributed among these distances:
57 26 0.28
58 19 0.20
59 41 0.44
60 8 0.09
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.33
Consensus pattern (56 bp):
ATAGTTTAGGATGAAATTGAAATATTCAAAAGTTTGAAGAACAATTTAGAATGGTC
Found at i:30245 original size:47 final size:50
Alignment explanation
Indices: 30176--30276 Score: 163
Period size: 47 Copynumber: 2.1 Consensus size: 50
30166 TTTATTTTCA
30176 TTTTTTCGAATAAACGCATGCGAATTAGATATCATGCGGTTAGG-TTTAT
1 TTTTTTCGAATAAACGCATGCGAATTAGATATCATGCGGTTAGGATTTAT
* *
30225 TTTTTTTGAAT-AA-GCATGCGAATTAGATATCATGCGGTTAGGATTTCT
1 TTTTTTCGAATAAACGCATGCGAATTAGATATCATGCGGTTAGGATTTAT
30273 TTTT
1 TTTT
30277 GTGGATAACA
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
47 29 0.59
48 10 0.20
49 10 0.20
ACGTcount: A:0.27, C:0.11, G:0.20, T:0.43
Consensus pattern (50 bp):
TTTTTTCGAATAAACGCATGCGAATTAGATATCATGCGGTTAGGATTTAT
Found at i:39970 original size:13 final size:13
Alignment explanation
Indices: 39929--39963 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
39919 CTTGAAGAAG
*
39929 AAATAAAAAAAGA
1 AAATGAAAAAAGA
*
39942 AAAAGAAAAAAGA
1 AAATGAAAAAAGA
39955 AAATGAAAA
1 AAATGAAAA
39964 TGAAAAAAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.83, C:0.00, G:0.11, T:0.06
Consensus pattern (13 bp):
AAATGAAAAAAGA
Found at i:39971 original size:27 final size:26
Alignment explanation
Indices: 39941--40049 Score: 71
Period size: 27 Copynumber: 4.1 Consensus size: 26
39931 ATAAAAAAAG
39941 AAAAAGAAAAAAGAAAATGAAAATGAA
1 AAAAAGAAAAAAGAAAA-GAAAATGAA
* *
39968 AAAAGGAGGAAAATG-AAAGAAAATGAA
1 AAAA--AGAAAAAAGAAAAGAAAATGAA
* *** *
39995 AAATGAGAAAAAATGAAAA-ATGGTGGA
1 AAA-AAGAAAAAA-GAAAAGAAAATGAA
* *
40022 AAAAAGAAAAATGAAGA-AAAATGAA
1 AAAAAGAAAAAAGAAAAGAAAATGAA
40047 AAA
1 AAA
40050 TGAAAAATAT
Statistics
Matches: 61, Mismatches: 16, Indels: 12
0.69 0.18 0.13
Matches are distributed among these distances:
25 11 0.18
26 13 0.21
27 24 0.39
28 6 0.10
29 7 0.11
ACGTcount: A:0.71, C:0.00, G:0.20, T:0.09
Consensus pattern (26 bp):
AAAAAGAAAAAAGAAAAGAAAATGAA
Found at i:39997 original size:17 final size:17
Alignment explanation
Indices: 39950--40054 Score: 85
Period size: 17 Copynumber: 6.2 Consensus size: 17
39940 GAAAAAGAAA
39950 AAAGAAAATG-AAAATG
1 AAAGAAAATGAAAAATG
*
39966 AAA-AAAGGA-GGAAAATG
1 AAAGAAA--ATGAAAAATG
39983 AAAGAAAATGAAAAATG
1 AAAGAAAATGAAAAATG
40000 AGAA-AAAATGAAAAATG
1 A-AAGAAAATGAAAAATG
*** *
40017 GTGGAAAAAAGAAAAATG
1 AAAG-AAAATGAAAAATG
40035 -AAGAAAAATGAAAAATG
1 AAAG-AAAATGAAAAATG
40052 AAA
1 AAA
40055 AATATAAAAC
Statistics
Matches: 72, Mismatches: 8, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
15 3 0.04
16 5 0.07
17 45 0.62
18 19 0.26
ACGTcount: A:0.69, C:0.00, G:0.21, T:0.10
Consensus pattern (17 bp):
AAAGAAAATGAAAAATG
Found at i:41489 original size:51 final size:51
Alignment explanation
Indices: 41424--41797 Score: 487
Period size: 51 Copynumber: 7.1 Consensus size: 51
41414 AAGCAAATTC
41424 GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
1 GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
*
41475 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
1 GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
41526 GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
1 GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
*
41577 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
1 GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
* * * **
41628 GTTTGTTGAAGATTGTTCGAGTTCTATATTCTCTGAAGGAATAGAGAGCGGACCC
1 GTTTGTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
* * * * *
41683 GTTTGTTGAAGATTATTCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGACAC
1 GTTTGTTGAAG---ATT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
* * * * *
41738 GTTTGTTGAAGATTGTTTGAGTCTTATACTCCCTGAATGAATAGGGAGCAGACAC
1 GTTTGTTGAAGA----TTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
41793 GTTTG
1 GTTTG
41798 CCAAAGATTG
Statistics
Matches: 294, Mismatches: 18, Indels: 18
0.89 0.05 0.05
Matches are distributed among these distances:
51 161 0.55
52 1 0.00
54 2 0.01
55 127 0.43
56 2 0.01
58 1 0.00
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (51 bp):
GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
Found at i:41805 original size:55 final size:55
Alignment explanation
Indices: 41423--41861 Score: 428
Period size: 55 Copynumber: 8.3 Consensus size: 55
41413 GAAGCAAATT
* * *
41423 CGTTTGTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAGACA
* * * * *
41474 AGTTCGTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAGACA
* * * *
41525 AGTTTGTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAGACA
* * * * *
41576 AGTTCGTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAGACA
* * * * * *
41627 AGTTTGTTGAAGATTGTTCGAGT-TCTATATTCTCTGAAGGAATAGAGAGCGGACC
1 CGTTTGTTGAAGATTGTTCGAGTCT-TATACTCCCTGAAGGAATAGGGAGCAGACA
* *
41682 CGTTTGTTGAAGATTATTCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGACA
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAGACA
* *
41737 CGTTTGTTGAAGATTGTTTGAGTCTTATACTCCCTGAATGAATAGGGAGCAGACA
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAGACA
*** * * * *
41792 CGTTTGCCAAAGATTGTTCGAGTCTTATACTCCTTGAAAGAAAAGGGAGCAGACC
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAGACA
41847 CGTTAT-TTGAAGATT
1 CGTT-TGTTGAAGATT
41862 TTTCAAGTAT
Statistics
Matches: 350, Mismatches: 31, Indels: 10
0.90 0.08 0.03
Matches are distributed among these distances:
51 161 0.46
54 2 0.01
55 185 0.53
56 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (55 bp):
CGTTTGTTGAAGATTGTTCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAGACA
Found at i:51944 original size:13 final size:13
Alignment explanation
Indices: 51926--51959 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
51916 AAAAAATTAC
51926 AGCAGCCCCCCTT
1 AGCAGCCCCCCTT
51939 AGCAGCCCCCCTT
1 AGCAGCCCCCCTT
51952 AGCAGCCC
1 AGCAGCCC
51960 ATGTGTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.18, C:0.53, G:0.18, T:0.12
Consensus pattern (13 bp):
AGCAGCCCCCCTT
Found at i:55249 original size:15 final size:16
Alignment explanation
Indices: 55221--55252 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
55211 AAAATCTTTC
55221 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
55237 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
55252 T
1 T
55253 GGATCTGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.06, C:0.25, G:0.19, T:0.50
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:56169 original size:12 final size:13
Alignment explanation
Indices: 56146--56189 Score: 81
Period size: 13 Copynumber: 3.5 Consensus size: 13
56136 AAAAAATTAC
56146 AGCAGCCCCCCTT
1 AGCAGCCCCCCTT
56159 AGCAG-CCCCCTT
1 AGCAGCCCCCCTT
56171 AGCAGCCCCCCTT
1 AGCAGCCCCCCTT
56184 AGCAGC
1 AGCAGC
56190 ACATGTGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.40
13 18 0.60
ACGTcount: A:0.18, C:0.50, G:0.18, T:0.14
Consensus pattern (13 bp):
AGCAGCCCCCCTT
Done.